Sequence threading

Fig. 6. Multiple threads in NAMD 2 allow the integration algorithm to be expressed sequentially as a single function. This function, shown illegibly at left, runs in sequencer threads associated with home patches. A similar function running in a controller thread on the master node communicates with the sequencers to deal with output and global calculations. Compute objects execute in the larger stack space of each node s main thread.

L Jaroszewski, L Rychlewski, B Zhang, A Godzik. Fold prediction by a hierarchy of sequence, threading, and modeling methods. Protein Sci 6 1431-1440, 1998. 

WR Taylor. Multiple sequence threading An analysis of alignment quality and stability. J Mol Biol 269 902-943, 1997. 

The ability to recognize the way in which a protein sequence is folded in three dimensions should enable us to model the interactions of specific side-chains in a manner that is simply not possible when considering proteins entirely at the sequence level. This notion has resulted in sequence threading algorithms that assess the level of compatibility of a sequence with a database of fold patterns (65, 66). The principal downside to this approach is that novel structural types cannot be pre- dieted, because at least one example of each fold type must be present in the fold pattern database. Structural genomics may be the means whereby fold pattern databases can be populated with sufficient data to make them useful as predictive tools. 

D. T. Jones, R. T. Miller, J. M. Thornton. Successful protein fold recognition by optimal sequence threading validated by rigorous blind testing. Proteins. 1995, 23, 387-397. 

SSThread http //www.ddbj.mg.ac.jp/E-maLl/ssthread/www service.html Sequence threading... 

Figure 34 Computer-generated model of the Sw2 sequence threaded onto a coiled coil (left) and a zinc-finger (right) backbone. (Reproduced from Ref 106. American Chemical Society, 2006.)...

The statistical analysis employs only native structures, whereas our LP protocol is using sequences threaded through wrong structures (misthreaded)... 

Based on the fact that 200 sequences threaded through 1000 structures take 1 CPU day on an SGI Origin 200. 

Ithough knowledge-based potentials are most popular, it is also possible to use other types potential function. Some of these are more firmly rooted in the fundamental physics of iteratomic interactions whereas others do not necessarily have any physical interpretation all but are able to discriminate the correct fold from decoy structures. These decoy ructures are generated so as to satisfy the basic principles of protein structure such as a ose-packed, hydrophobic core [Park and Levitt 1996]. The fold library is also clearly nportant in threading. For practical purposes the library should obviously not be too irge, but it should be as representative of the different protein folds as possible. To erive a fold database one would typically first use a relatively fast sequence comparison lethod in conjunction with cluster analysis to identify families of homologues, which are ssumed to have the same fold. A sequence identity threshold of about 30% is commonly... 

Bryant S H and C E Lawrence 1993. An Empirical Energy Function for Threading Protein Sequences Through the Folding Motif. Proteins Structure, Punction and Genetics 16 92-112. 

As the second educt (B), the plasmid ONA with complementary sticky ends is prepared separately. In the first step the isolated plasmid DNA is cut open by a special type of enzyme called restriction endonuclease. It scans along the thread of DNA and recognizes short nucleotide sequences, e.g., CTGCAG, which ate cleaved at a specific site, e.g., between A and G. Some 50 of such enzymes are known and many are commercially available. The ends are then again extended witfa he aid of a terminal transferase by a short sequence of identical nucleotides complementary to the sticky ends of educt (A). 

This section briefly reviews prediction of the native structure of a protein from its sequence of amino acid residues alone. These methods can be contrasted to the threading methods for fold assignment [Section II.A] [39-47,147], which detect remote relationships between sequences and folds of known structure, and to comparative modeling methods discussed in this review, which build a complete all-atom 3D model based on a related known structure. The methods for ab initio prediction include those that focus on the broad physical principles of the folding process [148-152] and the methods that focus on predicting the actual native structures of specific proteins [44,153,154,240]. The former frequently rely on extremely simplified generic models of proteins, generally do not aim to predict native structures of specific proteins, and are not reviewed here. 

SH Bryant, CE Lawrence. An empirical energy function for threading protein sequence thi-ough the folding motif. Pi-otems Struct Eunct Genet 16 92-112, 1993. 

TR Defay, EE Cohen. Multiple sequence information for threading algorithms. J Mol Biol 262 314-323, 1996. 

Threading methods can assign amino acid sequences to known three-dimensional folds... 

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